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The only thing holding me back from playing Settlers with BOTH the Traders and Barbarians set and the Seafarers set at once is the thought of sorting the pieces out at the end and getting everything back into the correct boxes. Is there a marking method out there that does not mar the beauty of the pieces but makes packing-up easier?

Keep in mind that some scenarios in Seafarers call for a stack of shuffled upsidedown tiles to be drawn from during the game. You wouldn't want any of those tiles to be marked.
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GregMay 9 '11 at 19:50

We colored coded the items from each set using colored markers on the thin white side edge of each of the hexes, board pieces, etc based on the set with which it had arrived. We used light pastel markers, the effect is not noticable during standard game play but makes it incredibly easy to group cards at the end of the gam

To simplify, I recommend the original game items be left white and the other pieces be filled in....

I would just write down how much of what you need in each box and use that as a check list. If you remember what the pieces are called, a list is easier to make and doesn't require printing. Separating how many times of each tile goes in the Seafarers box and the base game box is a hassle. I've already put a list of components in my 5-6 player boxes for the extensions, but not in my Seafarers main expansion box. Next time I play Seafarers I'm going to add one.

I don't have the Traders and Barbarians expansion, but assuming it doesn't come with a list of components, you could do the following:

If you have a digital camera and a color printer, you could take one of each component from an expansion, group them together and take a picture of the components, print off a copy of the picture, and keep that picture with your expansion box. Repeat for each expansion.

Then, when it is time to pick up, just refer to the picture list of components of where everything needs to go.

If you don't have a digital camera, I'm sure you could find images doing a Google Image Search for all the components.

There a few easy solutions such as putting stickers on the back of terrain hexes and border pieces, either color coded or with, say, "S" written on them for Seafarers, "C" for C&K et cetera. The previous "light marker on hex edges" suggestion above was brilliant as well. Maintaining a count of how many types of each hex go where isn't too difficult to begin with, considering each box lists on the back or in the manual exactly what comes in it. Further, virtually each expansions offerings are unique to it. As long as you have the same edition, all your basic resource tile are going to look the same, it seems a tad neurotic to worry about which box an individual hex came from.

There are easy solutions as mentioned, but the best advice I can give you is not to care, because the power of Catan lies in its variance and your creativity. For example, my friends' set includes Settlers, Seafarers, and both respective 5-6 player expansions. They mixed them all together as soon as they were out of the boxes, and are all stored in whichever boxes provide the neatest, most efficient fit. We just leave all the player piece bags in one area so everyone can pick from all six colors, rather than worry about leaving brown and green in the 5-6 box and unless we use all the others first. Here is how we begin every game:

We discuss what kind of game we want to play based on number of players and time available which basically just means which of the available special rules we wish to use.

We choose from ALL available border pieces, and assemble a good size (mostly we go as big as possible) into an interesting shape.

If we're using ocean tiles (90% of the time we are) now, we'll throw those down, leaving the empty spaces as the shape of our landmasses.

After counting how many spaces, we decide how much of each resource hex will be shuffled into a stack. The tiles are then placed totally randomly or with a few dedicated placements (for example, we usually don't place gold hexes on islands a player can set up)

Work out a number spread based on how many tiles we have, count out numbers, shuffle randomly and place using the inward spiral technique from the rules. Adjust so no 6's and 8's border each other or are too concentrated in any region.

This process ensures different and relatively balanced games every time. I highly recommend instead of maintaining everything in a separate box and with a different rule set in mind for each, instead consider yourself to be an artist expanding their palette. All you art supplies are kept together, because you might only want to use the tiniest inclusion of one rule set (like adding in bridges or river tiles) or you might want to throw everything in on top of something else, like a full C&K scenario that takes place on an massively epic island archipelago.